I am a MEGAN user and I am deciding on thresholds to use for the annotation of metagenomic reads. I performed a test, blasting (using last+) the same sequence dataset using the same evalue, but different maximum number of maximum hits. Increasing the number of blastx hits from 2 to 10 led to a decrease (by about half) in the number summarized reads for each taxa.
Does anyone know why that would happen?